CRISPR-Cas9 Gene Editing Technology: Will it Revolutionize Biology?

CRISPR

Imagine being able to make mutations in any gene you wanted say in stem cells in a relatively simple, quick and affordable fashion?

Sounds exciting, huh?

Every so often a new kind of technology comes along in the biomedical sciences that is a true game changer.

I’m talking about revolutionary technologies. Think ES cells and knockout mice, PCR, and iPS cells.

Many of the biomedical scientists I know are raving about a relatively new technology for genome editing that they believe belongs in this vaunted techno hall of fame: CRISPR-Cas9.

What the heck is CRISPR-Cas9?

Why are biomedical scientists scrambling excitedly to try it?

CRISPR-Cas9, mentioned first by Nature in its list of top science innovations of the past year, is basically a simple, but powerful new laboratory technology for editing the genome.

Sometimes the best innovations such as CRISPR-Cas9 have that unique combo of simplicity and power.

Bacteria use CRISPRs (clustered regularly interspaced palindromic repeats; see image above from Wikipedia) naturally as an anti-viral defense immunity mechanism. In that natural context, CRISPR DNA sequences are transcribed into CRISPR RNAs that in turn can lead to the destruction of very specific viral DNA sequences via the Cas9 nuclease.

Clever researchers figured out that man-made CRISPR-Cas9s could be produced to work in mouse and human cells as powerful gene editing tools.

In fact, they can also be used to make very discrete mutations in the genome rather than just for destroying DNA. The ability of CRISPRs to rather simply make specific mutations makes conventional gene editing technologies (e.g. the basic methods for making knockout mice that for example my lab has used for many years) seem slow and clunky. What this means is that biomedical scientists can quickly and easily edit the genomes of cells such as ES cells and in turn even organisms such as mice via those ES cells. CRISPR technology should be far superior to traditional methods of making mutations in genomes or knockout mice.

Other new adaptations of CRISPR-Cas9 are already coming out including methods for turning the transcription of specific loci ON or OFF with dCas9 (nuclease deficient) fusions with repression or activation domains. Very cool.

The technology is being commercialized by a commercial venture Editas Medicine and will compete with existing zinc-finger nuclease technology that is used to do the same kinds of things. Interestingly, Nature quotes a leader in the zinc-finger arena as follows:

“CRISPR has taken the academic world by storm, and it’s a very exciting new technology,” says Philip Gregory, chief scientific officer of Sangamo. But, he says, there are still several kinks to be resolved, including studies that suggest that Cas9 can make cuts at off-target sites in the genome. Zhang says that his group and others are working on increasing the enzyme’s specificity, and have already made some gains.

Gregory shows CRISPR some respect, but also rightly points out some hurdles remain for CRISPR-Cas9. So like everything in life there are challenges too.

One of the biggest challenges here is specificity.

There are reports that Cas9, the enzyme effector of CRISPR, can sometimes cut in the wrong place in the genome. Also, unlike other genome editing methods where there is a selectable marker such as NEO for positive selection and DTA for negative selection against integrations in the wrong place in the genome, CRISPR-Cas9 has no selection capability at this point at all. So there is a bit of flying blind with it so far. I bet that these issues will be ironed out, but let’s see. Update: It’s also important to note as pointed out by a commenter (hat tip to Zeeshan) that the same issues w/lack of selection power apply to ZFs and TALENs.

So at this point I’d say CRISPR-Cas9 shows the potential to be a truly transformative new technology. It’ll be exciting to see how it evolves in the next few years.

8 thoughts on “CRISPR-Cas9 Gene Editing Technology: Will it Revolutionize Biology?


  1. Dr. Knoepfler,
    I have seen quite a few articles recently regarding the CRISPR-Cas9 gene editing system. Most of these articles present the system and it’s gene editing capabilities as simply amazing and new. Kudos to you for presenting a more balanced perspective especially with respect to the specificity challenges yet to be overcome. I’m assuming that researchers are mostly excited over having a tool other than Zinc finger proteins to work with do to the IP strangle that Sangamo has on Zinc fingers? I know the CRISPR-Cas9 system is easier to design, however, as you mentioned off target effects currently make human clinical work difficult at best and probably unlikely until specificity can be greatly improved. Is there any other potential advantage to the CRSPR-Cas9 system compared to Zinc Finger proteins other than the simplicity of design and/or freedom to operate with respect to IP?


  2. Please revise this statement as it is factually incorrect:

    “Also, unlike other genome editing methods where there is a selectable marker such as NEO for positive selection and DTA for negative selection against integrations in the wrong place in the genome, CRISPR-Cas9 has no selection capability at this point at all. So there is a bit of flying blind with it so far.”


      • Yes of course. The selectable markers used for positive or negative selection are almost always part of the homology donor used to introduce reporters/mutations into the genome. Hence, selection cassettes fairly independent of the technology being used to introduce them into the genome. Regardless of whether you’re using zinc fingers, TALENs or CRISPRs to introduce changes in the genome, the homology donor remains the same and one can put whichever selection cassette they choose on this donor.

        So the problem of not having selection cassettes, or the advantage of having them on the homology donor is not specific to CRISPRs, rather it is common to all genome editing technologies.


        • Unless I misunderstood the technology, there is no use of selectable markers at all with CRISPR-Cas9 technology at any step. The homology is in the tiny guide RNAs and if one wants to make point mutations in 100-something bp oligos. There is no way that I’ve heard of that selectable marker cassettes can be included with CRISPR-Cas9 system introduction into eukaryotic cells. If you have an example otherwise please link to it so we can clear it up.


          • It depends on what one is trying to do. For making reporter lines, one can certainly include selection cassettes. An example of this is in figure 4 of this paper:
            http://www.pnas.org/content/early/2013/08/09/1313587110.full.pdf

            However, if one is using oligonucleotides or introducing deletions without homologous recombination, then you can’t do selection. But this limitation is not specific for CRISPR-Cas9 at all; one would be faced with the same issue if using Zinc fingers or TALENs to do the same.


            • Thanks for the helpful context and link. I’ve now added a mention to the post that the same issues w/lack of selection apply to ZFs and TALENs.

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